DOI Manager

docs/source/editor/prepub.rst

@@ -33,14 +33,15 @@ Check the ‘Mark as Complete’ box to move onto the next step.
 3. Verify DOIs
 --------------
 
-Articles usually have a DOI, or Digital Object Identifier, automatically assigned and ‘minted’ (created) for them by the system. This unique digital link to the article is usually created automatically for you by the system, and the Verify DOI stage lets you check if the DOI has been issued successfully or if there are any problems.
-If the DOI only has two ‘hops’, or two steps shown as bullet points in the Verify DOI stage, this means that no further changes are needed and you are ready to proceed. 
-You can verify that the article’s DOI is resolving correctly by clicking ‘Edit’ in the top right hand corner of the pop up window and checking that the ‘Status’ column reads ‘Success’. If the DOI Status is listed as pending, or blank, click ‘Poll for DOI Status’. If no DOI has been assigned, click ‘Issue DOI’. NB that newly issued DOIS can take a while to go through.  
+Articles usually have a DOI (Digital Object Identifier) automatically assigned and ‘minted’ (created) for them by the system. The DOI serves both as a unique identifier and a permalink. The ‘Verify DOI’ step lets you check if the DOI is working successfully as a permalink.
 
+If the DOI only has two ‘hops’, or two steps (shown as bullet points), this means that no further changes are needed and you are ready to proceed.
+
+If the DOI has more than two hops, or you see something else, you need to look more closely at the DOI's details. Select ‘Edit’ in the top right hand corner of the pop up window and check the ‘Status’ column for an indication of what to do next. See :ref:`Interpreting Registration Status<interpreting-registration-status>` for more help.
 
 .. figure:: ../nstatic/prepubgif2.gif
 
-Check the ‘Mark as Complete’ box to move onto the next step. 
+Check the ‘Mark as Complete’ box to move onto the next step.
 
 4. Select a Galley for Rendering
 --------------------------------

docs/source/manager.rst

@@ -13,7 +13,7 @@ Manager
    manager/submission/index
    manager/content/index
    manager/articlesissues/index
-   manager/crossref/index
+   manager/identifiers/index
    manager/users/index
    manager/other/index
 

docs/source/manager/identifiers/index.rst

@@ -0,0 +1,119 @@
+Identifiers
+===========
+
+Support for minting Digital Object Identifiers (DOIs) with Crossref is built into Janeway's core. We will be expanding this to other providers in the future.
+
+When Are DOIs Minted?
+---------------------
+If all the settings are properly configured (see below), Janeway handles DOI registration for you, stepping in at a few key points in the publishing pipeline.
+
+By default, a DOI is registered (a.k.a. minted, deposited) with Crossref when an article is accepted for publication. Some provisional metadata is sent at this time. 
+
+.. tip::
+    You can let editors see a preview of the data that gets sent before accepting an article. See **Accept Article Warning** under :ref:`Review Settings<reviewsettings>`.
+
+At this stage, the DOI will be registered with Crossref, but the webpage it points to on your journal website may not be active yet if the article isn't published yet. That's normal.
+
+The DOI is deposited with Crossref again when the article is published, so any metadata updated in the interim will also be updated in Crossref's metadata feeds. This is also when the DOI starts working as a permalink, in addition to being a unique identifier.
+
+There are things that might interrupt this default behavior. If you are importing backlist content, or there's an issue with the Crossref settings entered, or the required metadata isn't there, you may need to take a more active role. That's where the DOI Manager comes in.
+
+.. _doimanager:
+
+DOI Manager
+-----------
+You can see all the DOIs for a journal (if you are an editor) or for a press (if you are a staff member) in the DOI Manager.
+
+First, filter by date, registration status, or primary issue until you have an actionable set of articles.
+
+In some cases, you can preview the XML that will get sent to Crossref.
+
+Once you have filtered the articles to your liking, you can take two actions: **Register DOIs** and **Poll for status**. **Register DOIs** will package up all the metadata into XML and send it to Crossref. Crossref will put all the deposits they receive in a queue to process, so the status may not be immediate. After a few moments (or longer if it is a large batch), you can use **Poll for status** to check the result.
+
+.. warning::
+    **Poll for status** on a large group of articles could take a long time, so test it out on a smaller group first.
+
+.. _interpreting-registration-status:
+
+Interpreting Registration Status
+--------------------------------
+
+Unknown
+    Janeway doesn't know the status. Try **Poll for status**.
+
+Not yet registered
+    This DOI hasn't been registered yet. You can register it if what you see in the **DOI** column looks right (including pattern previews).
+
+Queued at Crossref
+    The deposit batch you sent is waiting to be read by the Crossref servers.
+
+Registered
+    Success! Crossref understood all the metadata you sent and didn't find any problems with it. 
+
+.. tip::
+    A status of **Registered** does not necessarily mean that the DOI will resolve correctly, if the URL it points to isn't fully operational yet on the Janeway side (i.e., the article isn't published).
+
+Registered (but some citations not correctly parsed)
+    Crossref understood the article-level metadata, but when it went to process the citations, there were errors. Check the XML in the **Response** column for details.
+
+Registered with warning
+    Crossref understood and registered the DOI, but sent back a warning. Check the XML in the **Response** column for details.
+
+Registration failed
+    Crossref tried to register the DOI but couldn't because of a problem. Check the XML in the **Response** column for details.
+
+Crossref Settings
+-----------------
+To edit the Crossref settings, select **Crossref Settings** from the manager interface. The fields are as follows:
+
+Use Crossref DOIs
+    If disabled, no DOIs will be minted
+
+Use Crossref Test Deposit Server
+    If enabled, DOIs will be minted on Crossref's test system
+
+Crossref Username
+    Your crossref username
+
+Crossref Password
+    Your crossref password
+
+Crossref Depositor Email
+    The email address of the depositor
+
+Crossref Depositor Name
+    The name of the depositor
+
+Crossref Prefix
+    The prefix for your crossref account -- usually 10.XXXX
+
+Crossref Registrant Name
+    The name of the registrant for this journal on Crossref's system (e.g. Open Library of Humanities)
+
+DOI Display Prefix
+    Text to prepend to DOIs -- used to generate DOI URLs
+
+DOI Display Suffix
+    Text to append to DOIs -- also used to generate DOI URLs
+
+DOI Pattern
+    The pattern for auto-generating DOIs. Defaults to using the journal code and article ID (e.g. orbit.123):
+
+        ``{{ article.journal.code }}.{{ article.pk }}``
+
+Crosscheck Settings
+-------------------
+Janeway also has support for Crosscheck (also called Similarity Check), which is provided by iThenticate. You can sign up for an account via Crossref and this will allow you to send submitted manuscripts for originality checking.
+
+The settings are:
+
+Enable
+    Enables display for Crosscheck buttons
+
+Username
+    Your iThenticate service username
+
+Password
+    Your iThenticate service password
+
+More info on Crosscheck/Similarity Check: https://www.crossref.org/services/similarity-check/

docs/source/manager/review/index.rst

@@ -5,6 +5,8 @@ The management interface has two sections that allow you to manage peer review s
 - Review Settings
 - Review Forms
 
+.. _reviewsettings:
+
 Review Settings
 ---------------
 Under review settings we can control how peer review operates for the given journal. The settings editable here are:

docs/source/published/articles.rst

@@ -56,14 +56,14 @@ Publisher notes appear on the article page below the abstract and how to cite bl
 
 Identifiers
 -----------
-Any identifiers such as DOIs are listed here and a link to manage them is in the top right of the block. From that link you can manage the identifiers.
+Any identifiers such as DOIs are listed here and a link to manage them is in the top right of the block.
 
 .. figure:: /nstatic/edit_doi.png
 
-    The identifiers manager
+    The article-level identifiers manager
 
-.. warning::
-    Janeway does not currently tell you if a DOI was deposited successfully, to do so you can test the DOI or check the issue admin system.
+.. tip::
+    You can also manage DOIs at the journal level as an editor (and at the press level as a staff user) using the :ref:`DOI Manager<doimanager>`.
 
 Galleys
 -------

src/core/forms.py

@@ -5,21 +5,24 @@
 
 import uuid
 import copy
+import functools
+import itertools
 
 from django import forms
 from django.forms.fields import Field
 from django.utils import timezone
 from django.utils.translation import ugettext_lazy as _, get_language
 from django.conf import settings
 from django.contrib.auth.forms import UserCreationForm
+from django.db.models import Q
 
 from django_summernote.widgets import SummernoteWidget
 
 from core import models, validators
 from utils.logic import get_current_request
 from journal import models as journal_models
 from utils import setting_handler
-from utils.forms import KeywordModelForm, JanewayTranslationModelForm, CaptchaForm
+from utils.forms import KeywordModelForm, JanewayTranslationModelForm, CaptchaForm, HTMLDateInput
 from utils.logger import get_logger
 from submission import models as submission_models
 
@@ -496,3 +499,123 @@ def save(self, commit=True):
             access_request.save()
 
         return access_request
+
+
+class CBVFacetForm(forms.Form):
+
+    def __init__(self, *args, **kwargs):
+        # This form populates the facets that users can filter results on
+        # If you pass a separate facet_queryset into kwargs, the form is
+        # the same regardless of how the result queryset changes
+        # To have the facets dynamically contract based on the result queryset,
+        # do not pass anything for facet_queryset into kwargs.
+
+        self.id = 'facet_form'
+        self.queryset = kwargs.pop('queryset')
+        self.facets = kwargs.pop('facets')
+        self.facet_queryset = kwargs.pop('facet_queryset', None)
+        if not self.facet_queryset:
+            self.facet_queryset = self.queryset
+        self.fields = {}
+
+        super().__init__(*args, **kwargs)
+
+        for facet_key, facet in self.facets.items():
+
+            if facet['type'] == 'foreign_key':
+
+                # Note: This retrieval is written to work even for sqlite3.
+                # It might be rewritten differently if sqlite3 support isn't needed.
+                if self.facet_queryset:
+                    column = self.facet_queryset.values_list(facet_key, flat=True)
+                else:
+                    column = self.queryset.values_list(facet_key, flat=True)
+                values_list = list(filter(bool, column))
+                choice_queryset = facet['model'].objects.filter(pk__in=values_list)
+
+                if facet.get('order_by'):
+                    choice_queryset = self.order_by(choice_queryset, facet, values_list)
+
+                choices = []
+                for each in choice_queryset:
+                    label = getattr(each, facet["choice_label_field"])
+                    count = values_list.count(each.pk)
+                    label_with_count = f'{label} ({count})'
+                    choices.append((each.pk, label_with_count))
+                self.fields[facet_key] = forms.ChoiceField(
+                    widget=forms.widgets.CheckboxSelectMultiple,
+                    choices=choices,
+                    required=False,
+                )
+
+            elif facet['type'] == 'charfield_with_choices':
+                # Note: This retrieval is written to work even for sqlite3.
+                # It might be rewritten differently if sqlite3 support isn't needed.
+
+                if self.facet_queryset:
+                    queryset = self.facet_queryset
+                else:
+                    queryset = self.queryset
+                column = []
+                values_list = []
+                lookup_parts = facet_key.split('.')
+                for obj in queryset:
+                    for part in lookup_parts:
+                        if obj:
+                            try:
+                                result = getattr(obj, part)
+                                obj = result
+                            except:
+                                result = None
+
+                    if result != None:
+                        values_list.append(result)
+                    elif result == None and 'default' in facet:
+                        values_list.append(facet['default'])
+
+                unique_values = set(values_list)
+                choices = []
+                model_choice_dict = dict(facet['model_choices'])
+                for value in unique_values:
+                    label = model_choice_dict.get(value, value)
+                    count = values_list.count(value)
+                    label_with_count = f'{label} ({count})'
+                    choices.append((value, label_with_count))
+                self.fields[facet_key] = forms.ChoiceField(
+                    widget=forms.widgets.CheckboxSelectMultiple,
+                    choices=choices,
+                    required=False,
+                )
+
+            # To do:
+            elif facet['type'] == 'date_time':
+                self.fields[facet_key] = forms.DateTimeField(
+                    widget=HTMLDateInput(),
+                    required=False,
+                )
+
+            elif facet['type'] == 'boolean':
+                pass
+
+            self.fields[facet_key].label = facet['field_label']
+
+    def order_by(self, queryset, facet, fks):
+        order_by = facet.get('order_by')
+        if order_by != 'facet_count' and order_by in facet['model']._meta.get_fields():
+            queryset = queryset.order_by(order_by)
+        elif order_by == 'facet_count':
+            sorted_fk_tuples = sorted(
+                [(fk, fks.count(fk)) for fk in fks],
+                key=lambda x:x[1],
+                reverse=True,
+            )
+            sorted_fks = [tup[0] for tup in sorted_fk_tuples]
+            queryset = sorted(
+                queryset,
+                key=lambda x: sorted_fks.index(x.pk)
+            )
+
+        # Note: There is no way yet to sort on the result of a 
+        # function property like journal.name
+
+        return queryset

src/core/include_urls.py

@@ -70,6 +70,7 @@
         name='serve_press_file',
         ),
     url(r'^press/merge_users/$', press_views.merge_users, name='merge_users'),
+    url(r'^doi_manager/$', press_views.IdentifierManager.as_view(), name='press_identifier_manager'),
 
     # Notes
     url(r'^article/(?P<article_id>\d+)/note/(?P<note_id>\d+)/delete/$', core_views.delete_note,

src/core/templatetags/classname.py

@@ -0,0 +1,11 @@
+from django import template
+
+register = template.Library()
+
+
+@register.filter
+def classname(obj):
+    try:
+        return obj.__class__.__name__
+    except AttributeError:
+        return ''